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Yorodumi- PDB-3abr: Crystal structure of ethanolamine ammonia-lyase from Escherichia ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3abr | ||||||
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Title | Crystal structure of ethanolamine ammonia-lyase from Escherichia coli complexed with CN-Cbl (substrate-free form) | ||||||
Components | (Ethanolamine ammonia-lyase ...) x 2 | ||||||
Keywords | LYASE / (beta/alpha)8 fold / Cobalt / Cobalamin | ||||||
Function / homology | Function and homology information ethanolamine ammonia-lyase / ethanolamine ammonia-lyase activity / ethanolamine ammonia-lyase complex / ethanolamine degradation polyhedral organelle / ethanolamine catabolic process / cobalamin binding / amino acid metabolic process / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Shibata, N. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2010 Title: Crystal structures of ethanolamine ammonia-lyase complexed with coenzyme B12 analogs and substrates. Authors: Shibata, N. / Tamagaki, H. / Hieda, N. / Akita, K. / Komori, H. / Shomura, Y. / Terawaki, S. / Mori, K. / Yasuoka, N. / Higuchi, Y. / Toraya, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3abr.cif.gz | 571.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3abr.ent.gz | 471.4 KB | Display | PDB format |
PDBx/mmJSON format | 3abr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3abr_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 3abr_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 3abr_validation.xml.gz | 66.1 KB | Display | |
Data in CIF | 3abr_validation.cif.gz | 93 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ab/3abr ftp://data.pdbj.org/pub/pdb/validation_reports/ab/3abr | HTTPS FTP |
-Related structure data
Related structure data | 3aboSC 3abqC 3absC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
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-Components
-Ethanolamine ammonia-lyase ... , 2 types, 4 molecules ACBD
#1: Protein | Mass: 49447.816 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b2441, eutB, JW2434 / Plasmid: pUSI2 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P0AEJ6, ethanolamine ammonia-lyase #2: Protein | Mass: 33197.031 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b2440, eutC, JW2433 / Plasmid: pUSI2 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P19636, ethanolamine ammonia-lyase |
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-Non-polymers , 4 types, 1015 molecules
#3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-NA / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.01 Å3/Da / Density % sol: 69.36 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.3 Details: 6.0-7.0% (w/v) PEG 4000, 24-26 % (v/v) glycerol, 1.0 % (v/v) 2-methyl-2,4-pentanediol (MPD), 0.1 M imidazole-HCl, pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 3, 2008 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. all: 144730 / Num. obs: 144730 / % possible obs: 94.6 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 2.1→2.15 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.299 / Mean I/σ(I) obs: 3.5 / Num. unique all: 9260 / % possible all: 91.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ID 3ABO Resolution: 2.1→42.29 Å / Cor.coef. Fo:Fc: 0.878 / Cor.coef. Fo:Fc free: 0.841 / SU B: 12.464 / SU ML: 0.162 / Cross valid method: THROUGHOUT / ESU R: 0.197 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.382 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→42.29 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.1→2.155 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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